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Package 214/467HostnameOS / ArchBUILDCHECKBUILD BIN
GSVA 1.0.1
Justin Guinney
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/GSVA
Last Changed Rev: 56241 / Revision: 59457
Last Changed Date: 2011-06-16 15:04:11 -0700 (Thu, 16 Jun 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  ERROR 

Summary

Package: GSVA
Version: 1.0.1
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GSVA_1.0.1.tar.gz
StartedAt: 2011-10-20 14:51:15 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:52:26 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GSVA.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GSVA.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSVA/DESCRIPTION' ... OK
* this is package 'GSVA' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'GSVA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compute.geneset.es: no visible binding for global variable
  'rank_scores'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   GSVA.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/GSVA.Rcheck/00check.log'
for details

GSVA.Rcheck/00install.out:

* installing *source* package 'GSVA' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"       -I/src/include -IC:/GSL/x64/include   -O2 -Wall  -std=gnu99 -c assess_density_test.c -o assess_density_test.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"       -I/src/include -IC:/GSL/x64/include   -O2 -Wall  -std=gnu99 -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"       -I/src/include -IC:/GSL/x64/include   -O2 -Wall  -std=gnu99 -c register_cmethods.c -o register_cmethods.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o GSVA.dll tmp.def assess_density_test.o ks_test.o register_cmethods.o -LC:/GSL/x64/lib -lgsl -lgslcblas -lm -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/GSVA.Rcheck/GSVA/libs/x64
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GSVA)

GSVA.Rcheck/GSVA-Ex.timings:

nameusersystemelapsed
computeGeneSetsOverlap000
filterGeneSets000
gsva0.920.000.97